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Alistair Bailey
I currently work as a learning technologist supporting Librarians at the University of Southampton.
An engineer by training, I have since worked primarily as an informatician and research scientist investigating antigen processing and presentation by major histocompatibility molecules.
My most recent project was CRUK Accelerator: Improving immunotherapy treatment for cancer patients. Other projects I have worked on include research into influenza, COVID19, skin sensitization to chemical allergens, asthma and contagious cancer in the Tasmanian Devil. I am also a Data and Software Carpentry instructor.
Education
Carpentries Instructor
Worldwide
The Carpentries
2017 - 2017
- I trained as a Carpentries instructor as part of their volunteer led mission to increase global capacity in essential data and computational skills for conducting efficient, open, and reproducible research.
Machine Learning
Stanford University
Coursera
2016 - 2016
- 10 week online introduction to machine learning.
Data Science Specialization
John Hopkins University
Coursera
2015 - 2015
- 12 month online set of courses on data science using R, git and command line tools.
PhD, Immunology
Cancer Sciences, University of Southampton
Southampton, UK
2013 - 2008
- Thesis: Relating the structure, function and dynamics of the MHC Class I antigen presenting molecule.
BEng, Civil Engineering
University of Southampton
Southampton, UK
2008 - 2005
- First Class Honours in Civil Engineering.
Engineering, Science & Mathematics Foundation Year
University of Southampton
Southampton, UK
2005 - 2004
- Maths and physics foundation year preparation for undergraduate study.
BTEC ND Audio-Visual Production
Bournemouth & Poole College of Art & Design
Bournemouth, UK
1994 - 1992
- Foundation course in film, photography, TV and radio production.
Research Experience
Research Fellow
Centre for Proteomic Research/Cancer Sciences, University of Southampton
Southampton, UK
2023 - 2018
- Cancer Research UK Accelerator: this project aims to identify potential treatment targets for hard to treat cancers such as lung cancer using peptidomics methods.
In my role, I process, analyse and manage data from various Omics technologies, primarily whole exome sequencing, RNAseq and proteomics. Proteomics data I receive as Thermo raw data and process with Peaks Studio, and post-process in R and RStudio. Whole exome and transcriptomics data I receive as fastq files and I use a mixture of command line tools using bash scripts and R and RStudio. I tend to follow the Broad Institute Best Practices for genomic data analysis and Cornell Bioinformatics Core for transcriptomic data processing. Scripts and processed data are managed using git version control. Raw data is backed up remotely and deposited along with processed outputs public repositories such as EBI PRIDE and the European Phenome-Genome Archive following FAIR protocols. My primary computer is a Linux Ubuntu machine, but I also use Windows. - We have also developed our method to identify treatment targets for infectious diseases such as influenza.
- In 2020 I also worked to develop a COVID19 test using proteomics methods.
Research Fellow
Centre for Proteomic Research/Cancer Sciences, University of Southampton
Southampton, UK
2018 - 2015
- Developed peptidomics methodology at the UoS for research into the role of MHC molecules in skin sensitisation to chemical allergy.
Research Fellow
Cancer Sciences, University of Southampton
Southampton, UK
2015 - 2013
- MRC Centenary Fellow
Industry Experience
I have worked in a variety of roles ranging from engineering to research scientist. I like collaborative environments where I can learn from my peers.
Internship
Microsoft Research
Cambridge, UK
2012 - 2012
- Helped develop computational model of MHC I peptide selection.
Freelance Satellite Communications Engineer
Globecast
London, UK
2012 - 2004
- I continued to work as an engineer in broadcast TV from 2004 and 2012 on major events such as the Olympics and Football World Cup.
Satellite Communications Engineer
Globecast
London, UK
2004 - 2000
- Full time engineer working in global broadcast TV primarily on sports, news and live entertainment events.
Film and television post-production engineer
Telecine
London, UK
2000 - 1995
- I trained as an engineer to operate various TV & film post-production equipment.
Teaching Experience
I am passionate about teaching foundational coding and data science skills to researchers and developing evidence-based best practices. I am especially interested in helping novices and making coding more accessible to all.
Software Carpentry
Umeå University
Umeå, Sweden
2018
- Taught R for Reproducible Research and assisted in Command Line Basics.
Data Carpentry
University of Southampton
Southampton, UK
2017
- Taught R for Reproducible Research and assisted in Command Line Basics and git.
Data Carpentry
University of Southampton
Southampton, UK
2017
- Taught R for Reproducible Research and assisted in introduction to SQL.
Software Carpentry
University of Southampton
Southampton, UK
2017
- Assisted with python and git for reproducible research.
British Society for Proteomics 2018 Data Science Workshop
University of Bradford
Bradford, UK
2018
- I created and taught a proteomics data science workshop including introduction to R, Volcano plots, heatmaps and peptide logos.
Coding Together
University of Southampton
Southampton, UK
2020 - 2019
- I created and taught an eight week series of collaborative workshops to teach foundational R coding and data science skills based on Carpentries materials.
Academic Support Tutor
IntoUniversity Millbrook
Southampton, UK
2019 - 2018
- IntoUniversity supports young people from disadvantaged backgrounds to attain either a university place or another chosen aspiration. I volunteered as an academic support tutor for secondary school learners.
Publications
Identification of neoantigens in esophageal adenocarcinoma
Immunology
N/A
2022
- Ben Nicholas, Alistair Bailey, Katy J. McCann, Oliver Wood, Robert C. Walker, Robert Parker, Nicola Ternette, Tim Elliott, Tim J. Underwood, Peter Johnson, Paul Skipp
Analysis of cell‐specific peripheral blood biomarkers in severe allergic asthma identifies innate immune dysfunction
Clinical & Experimental Allergy
N/A
2022
- Ben Nicholas, Jane Guo, Hyun‐Hee Lee, Alistair Bailey, Rene de Waal Malefyt, Milenko Cicmil, Ratko Djukanovic
The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers
PLOS Pathogens
N/A
2021
- Rachel S. Owen, Sri H. Ramarathinam, Alistair Bailey, Annalisa Gastaldello, Kathryn Hussey, Paul J. Skipp, Anthony W. Purcell, Hannah V. Siddle
Characterization of the Class I MHC Peptidome Resulting From DNCB Exposure of HaCaT Cells
Toxicological Sciences
N/A
2021
- Alistair Bailey, Ben Nicholas, Rachel Darley, Erika Parkinson, Ying Teo, Maja Aleksic, Gavin Maxwell, Tim Elliott, Michael Ardern-Jones, Paul Skipp.
Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands
PLoS Pathogens
N/A
2022
- Ben Nicholas, Alistair Bailey, Karl J. Staples, Tom Wilkinson, Tim Elliott, Paul Skipp.
The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif
Immunology
N/A
2021
- Annalisa Gastaldello, Sri H. Ramarathinam, Alistair Bailey, Rachel Owen, Steven Turner, N. Kontouli, Tim Elliott, Paul Skipp, Anthony W. Purcell, Hannah V. Siddle.
Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility
Frontiers in Immunology
N/A
2019
- Cory M. Ayres, Esam T. Abualrous, Alistair Bailey, Christian Abraham, Lance M. Hellman, Steven A. Corcelli, Frank Noé, Tim Elliott, Brian M. Baker.
Direct evidence for conformational dynamics in major histocompatibility complex class I molecules
JBC
N/A
2017
- Andy van Hateren, Malcolm Anderson, Alistair Bailey, Jörn M. Werner, Paul Skipp, Tim Elliott.
Recent advances in Major Histocompatibility Complex class I antigen presentation: Plastic MHC molecules and TAPBPR mediated quality control
F1000 Research
N/A
2017
- Andy van Hateren, Alistair Bailey, Tim Elliott.
Selector function of MHC I molecules is determined by protein plasticity
Scientific Reports
N/A
2015
- Alistair Bailey, Neil Dalchau, Rachel Carter, Stephen Emmott, Andrew Phillips, Jörn M. Werner, Tim Elliott
Two Polymorphisms Facilitate Differences in Plasticity between Two Chicken Major Histocompatibility Complex Class I Proteins
PLoS One
N/A
2014
- Alistair Bailey, Andy van Hateren, Tim Elliott, Jörn M. Werner.
A Mechanistic Basis for the Co-evolution of Chicken Tapasin and Major Histocompatibility Complex Class I Proteins
JBC
N/A
2013
- Andy van Hateren, Rachel Carter, Alistair Bailey, Nasia Kontouli, Anthony P. Williams, Jim Kaufman, Tim Elliott.
The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
Tissue Antigens
N/A
2010
- A. Van Hateren, E. James, A. Bailey, A. Phillips, N. Dalchau, T. Elliott